An example of an incorporation mix includes a liquid carrier, a complex, and a labeled nucleotide. The complex includes a polymerase and a plasmonic nanostructure linked to the polymerase. The labeled nucleotide includes a nucleotide, a 3′ OH blocking group attached to a sugar of the nucleotide, and a dye label attached to a base of the nucleotide.

An example of an incorporation mix includes a liquid carrier, a complex, and a labeled nucleotide. The complex includes a polymerase and a plasmonic nanostructure linked to the polymerase. The labeled nucleotide includes a nucleotide, a 3′ OH blocking group attached to a sugar of the nucleotide, and a dye label attached to a base of the nucleotide.

Described herein are synthetic methods for producing sequence-specific RNA oligonucleotides that eliminate impurities produced in prior art methods. In one aspect, an end-protected capture DNA complementary to a portion of the product RNA is employed. In another aspect, the template DNA is covalently or noncovalently linked to the RNA polymerase, either directly or through the use of a nontemplate DNA. In a third aspect, a flow chamber is employed. All of the methods can be used in combination.

Described herein are synthetic methods for producing sequence-specific RNA oligonucleotides that eliminate impurities produced in prior art methods. In one aspect, an end-protected capture DNA complementary to a portion of the product RNA is employed. In another aspect, the template DNA is covalently or noncovalently linked to the RNA polymerase, either directly or through the use of a nontemplate DNA. In a third aspect, a flow chamber is employed. All of the methods can be used in combination.

In an example, a flow cell includes a substrate, a selectively removable porous molecular network on the substrate and defining exposed substrate regions, and sequencing surface chemistry on at least some of the exposed regions. The sequencing surface chemistry is selected from the group consisting of i) an activated pad, a polymer layer attached to the activated pad, and a primer attached to the polymer layer; or ii) a nanostructure and an enzyme attached to the nanostructure.

In an example, a flow cell includes a substrate, a selectively removable porous molecular network on the substrate and defining exposed substrate regions, and sequencing surface chemistry on at least some of the exposed regions. The sequencing surface chemistry is selected from the group consisting of i) an activated pad, a polymer layer attached to the activated pad, and a primer attached to the polymer layer; or ii) a nanostructure and an enzyme attached to the nanostructure.

This invention provides a nanostructure device and method for the sequencing or identification of biomolecules based on in vitro template-directed enzymatic replication or synthesis.

This invention provides a nanostructure device and method for the sequencing or identification of biomolecules based on in vitro template-directed enzymatic replication or synthesis.

Methods for analyzing a nucleic acid molecule are described. Methods may include attaching the nucleic acid molecule to a particle having a first characteristic dimension. In addition, methods may include applying an electric field through an aperture to move the particle to the aperture. Also, methods may include applying a voltage across a first electrode and a second electrode. Further, methods may include contacting a portion of the nucleic acid molecule to both the first electrode and the second electrode within the aperture, where the portion may include a nucleotide. In addition, methods may include measuring a current through the first electrode, the portion of the nucleic acid molecule, and the second electrode, where the measured current runs in a direction parallel to a longitudinal axis of the aperture. Also, methods may include identifying the nucleotide of the portion of the nucleic acid molecule based on the current.

Methods for analyzing a nucleic acid molecule are described. Methods may include attaching the nucleic acid molecule to a particle having a first characteristic dimension. In addition, methods may include applying an electric field through an aperture to move the particle to the aperture. Also, methods may include applying a voltage across a first electrode and a second electrode. Further, methods may include contacting a portion of the nucleic acid molecule to both the first electrode and the second electrode within the aperture, where the portion may include a nucleotide. In addition, methods may include measuring a current through the first electrode, the portion of the nucleic acid molecule, and the second electrode, where the measured current runs in a direction parallel to a longitudinal axis of the aperture. Also, methods may include identifying the nucleotide of the portion of the nucleic acid molecule based on the current.